Fishermen and rescue workers hauled dozens of people out of the ocean after a ferry sank in the central Philippines on Friday, but at least two passengers drowned and 13 others were missing, authorities said.

In the latest disaster to hit the nation's notoriously dangerous sea
transport industry, the ferry mysteriously sank in calm weather before dawn about two kilometres (1.2 miles) from Burias island.

Local fishermen and volunteer coastguard personnel were the first to arrive, joined later by a navy plane, and 42 people were rescued throughout the morning, according to the authorities.

But national coastguard spokesman Armand Balilo said on radio station DZBB that the bodies of two women were recovered from the water and at least 13 others were missing.

Regional civil defence chief Raffy Alejandro said the cause of the sinking was not yet known but the ship's captain, who was among those rescued, reported the vessel may have been unbalanced by two passenger buses and a large truck it was carrying.

"He said it happened so quickly. It just went down in the darkness," Alejandro said, adding the waters and weather were calm.

The vessel was a roll-on, roll-off ferry commonly used in the Philippines to transport people, vehicles and cargo throughout the archipelago of more than 7,100 islands.

Alejandro said the ferry, the MV Lady of Mount Carmel, was not believed to have been overloaded as it sought to make its regular journey of about four hours between the two major provinces of Albay and Masbate, more than 300 kilometres southeast of Manila.

He said the ship was licensed to carry more than 200 passengers, while 57 people were listed on the manifest for Friday's trip.

Nevertheless, Balilo said that some more people were not on the list, a common practise in the Philippines, and that there may have been up to 62 on board.

Sea accidents are common in the Philippines due to poor safety standards and overloading.

The world's deadliest peacetime maritime disaster occurred near Manila in 1987 when a ferry laden with Christmas holidaymakers collided with a small oil tanker, killing more than 4,300 people.

In 2008, a huge ferry capsized during a typhoon off the central island of Sibuyan, leaving almost 800 dead.

Alejandro expressed hope that the death toll from Friday's accident would not rise drastically, partly because the captain said most passengers were wearing life jackets.

"We expect many more will be rescued. We were able to respond quickly," he said.